Mechanistic aspects of site-specific recombination were explored. To distinguish between models for the chemical step of recombination, alterations were made in nucleophiles that could potentially attack DNA. The evidence pointed to a symmetric mechanism for strand exchange in which a nucleophile from different protomers of a topoisomerase attack each partner in the recombination event. In a second study, the functional connection between two related proteins that cause DNA deformation was established and explored. The structural basis for the functional connection was demonstrated by showing that both proteins, which differ in their degree of DNA binding specificity, could assist the formation of the same nucleoprotein complex. A search for homologs of site-specific recombinases was refined. The sequence of candidate clones from S. pombe showed no significant homology to the target family and were judged to be coincidental matches to the probe. However, the clones did contain apparent homologs of the cerevisiae genes ARG4, ILV5 RPB6.